Question: Input file of NGS data for Pathview
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gravatar for amoltej
4.1 years ago by
amoltej90
Australia
amoltej90 wrote:

Hi, 

I have RNA seq data for different tissues of non-model insect. I want to visualize the pathway connection between these two tissues. for that I am planning to use pathview. But there is no clear cut example of input data set.

can someone please tell me what the input data should look like? and if any further information to get maximum out of pathview?

Thank you in advance

Amol

ADD COMMENTlink modified 4.1 years ago by xiaoheyiyh0 • written 4.1 years ago by amoltej90

There are some packages that do not work with non-model organisms, Pathview seems to be one of those, at least I didn't find it in the documentation at quick glance. There are more things you will need here: first you won't have pathway maps, so you need to a pathway reconstruction (KAAS could do that), based on the data and annotations you have, that can leave you with a highly fragmented pathway map (based on what?). Second, you need to make the package accept your own maps.

An alternative is to use drosophila maps and map your identifiers to drosophila genes. You might have better luck asking at https://support.bioconductor.org

ADD REPLYlink modified 18 days ago by RamRS25k • written 4.1 years ago by Dr. Mabuse47k

I Have already pathway maps from my transcript using iPathcon software. i have used drosophila dataset for that.

As you suggested I have posted question on bioconductor. Thank you for suggestion

Amol

ADD REPLYlink modified 18 days ago by RamRS25k • written 4.1 years ago by amoltej90
0
gravatar for xiaoheyiyh
4.1 years ago by
xiaoheyiyh0
United States
xiaoheyiyh0 wrote:

This question was answered at: https://support.bioconductor.org/p/73829/

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by xiaoheyiyh0
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